Contacts of the helix formed by residues 45 - 55 (chain A) in PDB entry 1X7O
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A VAL 4.2 0.4 + - - -
44A MSE 1.3 73.2 - - - +
46A VAL* 1.3 67.3 + - - -
47A ARG 3.2 3.1 + - - -
48A PRO* 3.4 6.2 - - - +
49A ILE* 3.1 28.7 + - - +
104A PRO* 4.8 5.0 - - - +
105A GLU 6.0 0.4 - - - -
106A VAL 3.2 16.6 + - - -
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY* 1.3 72.0 - - - +
47A ARG* 1.3 61.4 + - + +
49A ILE* 3.5 2.1 + - - +
50A SER* 2.9 34.3 + - - -
71A SER* 4.8 0.4 - - - +
73A TRP* 3.3 43.3 - - + -
74A ALA* 4.0 27.8 - - + +
77A LEU* 3.9 16.5 - - + +
105A GLU* 4.3 15.0 - - + +
106A VAL* 4.5 10.7 + - + +
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLY 3.2 0.2 - - - -
46A VAL* 1.3 82.8 - - + +
48A PRO* 1.3 72.0 - - + +
50A SER* 3.3 3.3 + - - -
51A LEU* 3.2 45.7 + - + +
73A TRP* 3.9 27.8 - - + -
174A THR* 2.9 41.5 + - - +
175A GLY* 4.6 0.4 - - - -
258B ALA* 3.9 30.3 + - - +
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Residues in contact with PRO 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 3.6 20.6 - - + -
44A MSE 3.4 15.9 - - - +
45A GLY* 3.4 11.9 - - - +
47A ARG* 1.3 97.7 - - + +
49A ILE* 1.3 60.1 + - - +
51A LEU* 3.3 8.1 + - + +
52A ALA* 3.0 18.5 + - - +
170A VAL* 5.7 2.9 - - + -
174A THR* 5.5 2.5 - - - -
175A GLY* 4.8 10.8 - - - +
178A PHE* 3.3 21.3 - - + -
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 3.7 22.4 - - + +
45A GLY 3.1 21.8 + - - +
46A VAL* 3.9 3.8 - - - +
48A PRO* 1.3 76.0 - - - +
50A SER* 1.3 63.6 + - - +
52A ALA* 3.1 6.4 + - - +
53A VAL* 3.0 30.3 + - + +
59A VAL* 5.2 2.5 - - + -
62A LEU* 4.1 17.9 - - + -
77A LEU* 4.1 19.1 - - + -
81A VAL* 5.7 0.2 - - + -
106A VAL* 3.6 37.5 - - + +
108A ALA* 3.7 28.9 - - + +
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL 2.9 14.3 + - - -
47A ARG 3.3 5.6 + - - -
49A ILE* 1.3 76.5 - - - +
51A LEU* 1.3 58.6 + - - +
53A VAL* 3.4 5.1 + - - +
54A GLU* 2.8 30.6 + - - +
73A TRP* 2.9 35.5 + - - -
77A LEU* 3.7 16.9 - - - +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 3.2 54.3 + - + +
48A PRO 3.7 7.2 - - - +
49A ILE 3.2 0.2 - - - -
50A SER* 1.3 76.7 - - - +
52A ALA* 1.3 64.8 + - - +
54A GLU* 3.6 21.5 - - - +
55A HIS* 3.0 42.3 + - + +
174A THR 4.5 0.4 - - - +
175A GLY* 3.9 23.1 - - - +
178A PHE* 3.7 14.3 - - + +
258B ALA* 5.4 9.6 - - + -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 5.3 0.2 - - + -
48A PRO 3.0 11.9 + - - +
49A ILE* 3.1 11.6 + - - +
51A LEU* 1.3 76.6 - - - +
53A VAL* 1.3 63.0 + - + +
55A HIS 3.4 0.3 + - - -
56A GLY 3.1 4.7 + - - -
57A TRP* 2.9 40.7 + - + +
59A VAL* 5.1 2.5 - - + -
110A VAL* 4.7 13.7 - - + -
178A PHE* 3.8 33.3 - - + -
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Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.0 22.6 + - + +
50A SER* 3.7 10.1 - - - +
52A ALA* 1.3 75.9 - - - +
54A GLU* 1.3 62.8 + - - +
56A GLY* 3.1 13.7 + - - -
57A TRP 4.6 4.7 - - - -
59A VAL* 3.9 23.1 - - + -
77A LEU* 4.9 2.0 - - + -
80A THR* 6.0 2.2 - - + -
81A VAL* 4.0 32.1 - - + -
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER 2.8 22.6 + - - +
51A LEU* 3.6 17.1 - - - +
52A ALA 3.3 0.2 - - - -
53A VAL* 1.3 76.3 - - - +
55A HIS* 1.3 80.7 + - - +
56A GLY 3.3 1.0 + - - -
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Residues in contact with HIS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.0 39.3 + - + +
52A ALA 3.7 0.2 - - - -
54A GLU* 1.3 99.5 + - - +
56A GLY* 1.3 60.3 + - - +
57A TRP* 3.5 11.6 + - + -
175A GLY 5.9 0.4 - - - -
178A PHE* 3.2 24.9 + - + +
179A SER* 3.4 31.5 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il